To design a well-thought out website, you must...think well! It's called "doing your PRIO" before you begin working on the actual coding for the site.

P--what is your Purpose? Why are you creating this website? What is it supposed to do?
R--who is your Reader? Are you targeting the 12 year olds, the 18-25 market, or the "over-the-hill gang" like your teacher? The answer to this will be a big factor in your choice of fonts, layouts, etc.
I--what is your Information? In this case, it's all the info you've gathered over the past few weeks for your project.
O--How will you organize your site. Before you ever begin writing code, you must have a clear idea in your mind and on paper of how things will connect.